create_blast_comparisons: Create blast comparisons for synteny plots

In djw533/micro.gen.extra: Microbial genomics extensions and functions

Create blast comparisons for synteny plots

Description

Create blast comparisons for synteny plots provided a list of fasta sequences, These can then be used as a readable format for genoplotR for synteny plots. The order of the fasta sequences will be the order of the genomic regions to be compared in the synteny plot from top to bottom. blastn and makeblastdb

Usage

create_blast_comparisons(
  blast_order,
  fasta_dir,
  blast_results_dir = "blast_results",
  overwrite = FALSE,
  color_scheme_name = "red_blue"
)

Arguments

blast_order	List of the fasta files to be compared, not including the ".fasta" extension.
fasta_dir	Directory where the fasta files are kept. If in the working directory, set this to "."
blast_results_dir	Directory to put the blast results into [Default = "blast_results"]
overwrite	TRUE/FALSE to overwrite a previously existing blast_results_dir [Default = FALSE]
color_scheme_name	color scheme to be used for the genoplotR comparison [Default = "red_blue"]

Value

a dna_comparisons list for genoplotR in addition to a directory with blast comparisons for a list of fasta sequences. Comparisons will be sequential. e.g. sequence_1 vs sequence_2, sequence_2 vs sequence_3, sequence_3 vs sequence_4

Examples

create_blast_comparisons(blast_order_list, "dir_with_fasta_files")

djw533/micro.gen.extra documentation built on Nov. 8, 2024, 5:11 a.m.